Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005714.1 Hibiscus syriacus cultivar Beakdansim tig00013355_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 96116
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Found at i:2519 original size:17 final size:17
Alignment explanation
Indices: 2497--2529 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
2487 CGACCATATT
2497 TTTTTTTATATTTTAAA
1 TTTTTTTATATTTTAAA
2514 TTTTTTTATATTTTAA
1 TTTTTTTATATTTTAA
2530 TAATAATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (17 bp):
TTTTTTTATATTTTAAA
Found at i:3410 original size:16 final size:16
Alignment explanation
Indices: 3385--3418 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
3375 ATTACATGTC
*
3385 AGGTTCATAACCAGTA
1 AGGTTCATAACAAGTA
*
3401 AGGTTGATAACAAGTA
1 AGGTTCATAACAAGTA
3417 AG
1 AG
3419 ATAATATCTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.41, C:0.12, G:0.24, T:0.24
Consensus pattern (16 bp):
AGGTTCATAACAAGTA
Found at i:16771 original size:14 final size:14
Alignment explanation
Indices: 16752--16782 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
16742 AATGAATTAA
16752 ATGAATAAATCTTC
1 ATGAATAAATCTTC
*
16766 ATGAATATATCTTC
1 ATGAATAAATCTTC
16780 ATG
1 ATG
16783 GCCAAATCCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.39, C:0.13, G:0.10, T:0.39
Consensus pattern (14 bp):
ATGAATAAATCTTC
Found at i:39951 original size:15 final size:16
Alignment explanation
Indices: 39928--39965 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
39918 TCTTTATACT
39928 AATTATTATA-ATTTA
1 AATTATTATATATTTA
*
39943 AATTTTTATATATTTA
1 AATTATTATATATTTA
*
39959 AAATATT
1 AATTATT
39966 TTGTGACCTA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
AATTATTATATATTTA
Found at i:40894 original size:24 final size:24
Alignment explanation
Indices: 40867--40913 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
40857 TAAAATACTA
40867 TTATTACACGTAATCAATATTAAT
1 TTATTACACGTAATCAATATTAAT
* * *
40891 TTATTTCACTTAATCAATGTTAA
1 TTATTACACGTAATCAATATTAA
40914 CTTTTCACAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.38, C:0.13, G:0.04, T:0.45
Consensus pattern (24 bp):
TTATTACACGTAATCAATATTAAT
Found at i:43020 original size:171 final size:171
Alignment explanation
Indices: 42730--43070 Score: 592
Period size: 171 Copynumber: 2.0 Consensus size: 171
42720 ATGAAGTCTC
* *
42730 TGATCCTTAGAATAATTCATATCATTGAGAAGATGCTTGGTATCCTTGATCCAATACACCCCAAC
1 TGATCCTTAGAATAATTCATATCATCGAGAAGATGCTTGGTATCCTCGATCCAATACACCCCAAC
* * *
42795 AGACGTGAATTCCCAAGTAAACCATCTAAAGTACTCTGTTACAATACGTAACATACTCTATGAAA
66 AGACGTGAATTCCCAAGTAAACCATATAAAGTACTCCGTTACAATACATAACATACTCTATGAAA
42860 TAGTAACACCAATGTCCTCTAGCTAAATCCTAACAGATCTA
131 TAGTAACACCAATGTCCTCTAGCTAAATCCTAACAGATCTA
* *
42901 TGATCCTTAGAATACTTCATATCATCGAGAAGATGCTTGGTATCGTCGATCCAATACACCCCAAC
1 TGATCCTTAGAATAATTCATATCATCGAGAAGATGCTTGGTATCCTCGATCCAATACACCCCAAC
* * *
42966 ATACGTGAATTCCCAAGTAAACCATATAAAGTACTCCGTTACATTACATAACATAGTCTATGAAA
66 AGACGTGAATTCCCAAGTAAACCATATAAAGTACTCCGTTACAATACATAACATACTCTATGAAA
43031 TAGTAACACCAATGTCCTCTAGCTAAATCCTAACAGATCT
131 TAGTAACACCAATGTCCTCTAGCTAAATCCTAACAGATCT
43071 CTGAAGTTAA
Statistics
Matches: 160, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
171 160 1.00
ACGTcount: A:0.36, C:0.24, G:0.12, T:0.28
Consensus pattern (171 bp):
TGATCCTTAGAATAATTCATATCATCGAGAAGATGCTTGGTATCCTCGATCCAATACACCCCAAC
AGACGTGAATTCCCAAGTAAACCATATAAAGTACTCCGTTACAATACATAACATACTCTATGAAA
TAGTAACACCAATGTCCTCTAGCTAAATCCTAACAGATCTA
Found at i:44171 original size:29 final size:29
Alignment explanation
Indices: 44146--44285 Score: 124
Period size: 29 Copynumber: 4.9 Consensus size: 29
44136 AGCAGAATCG
44146 GGACG-GGAATATAATCACATGTAGAAACA
1 GGACGAGG-ATATAATCACATGTAGAAACA
* *
44175 GGATGAGGATATAAT-ATCATATAGAAACA
1 GGACGAGGATATAATCA-CATGTAGAAACA
* * *
44204 GGACGATGATATAATCTCATGTAGAAATA
1 GGACGAGGATATAATCACATGTAGAAACA
* * * *
44233 GGACGGGGATATAATCCCATGCA-AAAAA
1 GGACGAGGATATAATCACATGTAGAAACA
* * * *
44261 AGATGGGGATATAATCACAAGTAGA
1 GGACGAGGATATAATCACATGTAGA
44286 TGACAGAAAT
Statistics
Matches: 90, Mismatches: 17, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
28 23 0.26
29 65 0.72
30 2 0.02
ACGTcount: A:0.44, C:0.11, G:0.24, T:0.21
Consensus pattern (29 bp):
GGACGAGGATATAATCACATGTAGAAACA
Found at i:50874 original size:2 final size:2
Alignment explanation
Indices: 50867--50901 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
50857 ATTAATGATA
50867 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
50902 GATAGATAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:50906 original size:4 final size:4
Alignment explanation
Indices: 50899--50981 Score: 166
Period size: 4 Copynumber: 20.8 Consensus size: 4
50889 ATATATATAT
50899 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
50947 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATA
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATA
50982 AACACATGAA
Statistics
Matches: 79, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 79 1.00
ACGTcount: A:0.51, C:0.00, G:0.24, T:0.25
Consensus pattern (4 bp):
ATAG
Found at i:53087 original size:19 final size:19
Alignment explanation
Indices: 53065--53105 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
53055 TCCTCTACTT
53065 TTTTATT-CATTTTTTCTCA
1 TTTTATTCCATTTTTTC-CA
*
53084 TTTTTTTCCATTTTTTCCA
1 TTTTATTCCATTTTTTCCA
53103 TTT
1 TTT
53106 ATTTTTTTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 11 0.55
20 9 0.45
ACGTcount: A:0.12, C:0.17, G:0.00, T:0.71
Consensus pattern (19 bp):
TTTTATTCCATTTTTTCCA
Found at i:53087 original size:20 final size:19
Alignment explanation
Indices: 53072--53110 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 19
53062 CTTTTTTATT
53072 CATTTTTTCTCATTTTTTTC
1 CATTTTTTC-CATTTTTTTC
53092 CATTTTTTCCATTTATTTT
1 CATTTTTTCCATTT-TTTT
53111 TTTCTTCTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.13, C:0.18, G:0.00, T:0.69
Consensus pattern (19 bp):
CATTTTTTCCATTTTTTTC
Found at i:53097 original size:8 final size:9
Alignment explanation
Indices: 53072--53105 Score: 50
Period size: 9 Copynumber: 3.6 Consensus size: 9
53062 CTTTTTTATT
53072 CATTTTTTC
1 CATTTTTTC
53081 TCATTTTTTTC
1 -CA-TTTTTTC
53092 CATTTTTTC
1 CATTTTTTC
53101 CATTT
1 CATTT
53106 ATTTTTTTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 12 0.52
10 4 0.17
11 7 0.30
ACGTcount: A:0.12, C:0.21, G:0.00, T:0.68
Consensus pattern (9 bp):
CATTTTTTC
Found at i:53522 original size:30 final size:30
Alignment explanation
Indices: 53457--53513 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
53447 GTGAACAATA
*
53457 AACAGTGCATCGATACGCTACAGTATCGTG
1 AACAGTGCATCGATACGCTACAGTAGCGTG
*
53487 AACAGTGCATCGATATGCTACAGTAGC
1 AACAGTGCATCGATACGCTACAGTAGC
53514 TGCTACAGTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.32, C:0.23, G:0.23, T:0.23
Consensus pattern (30 bp):
AACAGTGCATCGATACGCTACAGTAGCGTG
Found at i:53979 original size:47 final size:45
Alignment explanation
Indices: 53906--54030 Score: 155
Period size: 47 Copynumber: 2.8 Consensus size: 45
53896 ATAAAATCTT
* *
53906 TTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAAAATAC
1 TTACCATTTATTCCATAAGCTTGTAAGCTTATTTTACCAAAATAC
* *
53951 TTACCATTTAAATTCCATAAGCTTGTAAGCTTATTTTTCCAATATAC
1 TTACCATTT--ATTCCATAAGCTTGTAAGCTTATTTTACCAAAATAC
* *
53998 TTGCCA-TTATTCCGTAAGC-TGATAAGCTTATTT
1 TTACCATTTATTCCATAAGCTTG-TAAGCTTATTT
54031 GCATGGTTAC
Statistics
Matches: 71, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
43 2 0.03
44 21 0.30
45 9 0.13
46 2 0.03
47 37 0.52
ACGTcount: A:0.30, C:0.21, G:0.09, T:0.40
Consensus pattern (45 bp):
TTACCATTTATTCCATAAGCTTGTAAGCTTATTTTACCAAAATAC
Found at i:70602 original size:24 final size:24
Alignment explanation
Indices: 70574--70622 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
70564 AACATAAAAT
* *
70574 AATTGGATGAAACAAAAAAAATGA
1 AATTGAATAAAACAAAAAAAATGA
* *
70598 AATTGAATAAAATAAAATAAATGA
1 AATTGAATAAAACAAAAAAAATGA
70622 A
1 A
70623 GATAAAATAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.65, C:0.02, G:0.12, T:0.20
Consensus pattern (24 bp):
AATTGAATAAAACAAAAAAAATGA
Found at i:70948 original size:8 final size:9
Alignment explanation
Indices: 70920--70958 Score: 53
Period size: 9 Copynumber: 4.3 Consensus size: 9
70910 AACGTTAGGA
70920 AAATATAGT
1 AAATATAGT
*
70929 AAAAATAGT
1 AAATATAGT
70938 AAATA-AGT
1 AAATATAGT
70946 AAATATAGAT
1 AAATATAG-T
70956 AAA
1 AAA
70959 AAAATAATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
8 8 0.31
9 14 0.54
10 4 0.15
ACGTcount: A:0.64, C:0.00, G:0.10, T:0.26
Consensus pattern (9 bp):
AAATATAGT
Found at i:70948 original size:17 final size:19
Alignment explanation
Indices: 70920--70958 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 19
70910 AACGTTAGGA
70920 AAATATAGTAAAAATAG-T
1 AAATATAGTAAAAATAGAT
*
70938 AAATA-AGTAAATATAGAT
1 AAATATAGTAAAAATAGAT
70956 AAA
1 AAA
70959 AAAATAATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.64, C:0.00, G:0.10, T:0.26
Consensus pattern (19 bp):
AAATATAGTAAAAATAGAT
Found at i:71567 original size:37 final size:37
Alignment explanation
Indices: 71526--71630 Score: 147
Period size: 37 Copynumber: 2.8 Consensus size: 37
71516 ATGCTTGTGG
* * *
71526 ATCCTATCTTTAGGAGTTTAAATAATAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCATAGTAGAACTCT
* * * *
71563 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATTCT
1 ATCCTATTTTTAGGAGTTTGAATCATAGTAGAACTCT
71600 ATCCTATTTTTAGGAGTTTGAATCATAGTAG
1 ATCCTATTTTTAGGAGTTTGAATCATAGTAG
71631 GACGAAAAGG
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.31, C:0.13, G:0.15, T:0.40
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCATAGTAGAACTCT
Found at i:72566 original size:106 final size:106
Alignment explanation
Indices: 72381--73643 Score: 1804
Period size: 106 Copynumber: 12.0 Consensus size: 106
72371 CATTGTTCCA
* * * *
72381 AGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTTG-AATCGGGAAATTGTTTGTTGACAA
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC-TGAAATTGGGAAGTTGTTTGTTGACAA
* *
72445 CCAGTC-GTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
65 CCAG-CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTCG
* ** *
72487 AGTCCAATATCCTTTGTTGTGAAGTTGAAATTGGCTCCAAAATTGGGAAATTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAAC
*
72552 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTCG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTCG
* *
72593 AGTCCAATATACTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAAC
*
72658 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTCG
* * *
72699 AATCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTATGAAATTGAGAAGTTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAAC
72764 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC-CGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTC-G
* * * * *
72805 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATCGGGAAATTATTTGTTGACAAT
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAAC
* *
72870 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTCG
* * * * *
72911 AGTCAAATATCTTTCGCTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAAC
*
72976 CAGCGGTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCTCG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTCG
73017 AGTCCAATATCCTTCG-T-T---G-TG-AA---G-T-TGAAATTGGGAAGTTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAAC
* *
73070 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTCG
* * * *
73111 AGTCCAATATCCTTCGTTGTGAATTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAAA
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAAC
*
73176 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTCG
* * *
73217 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTATTTATTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAAC
* * *
73282 CAGCGGTCCCTTCGTCATGAAGTTGAACTTGCATTGTCTTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTCG
* * *
73323 AGTCCAATATCCTTCGTTGTGAAATTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAAC
* *
73388 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTAG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTCG
* * ** *
73429 AGTCTAATATCCTTCGTTGTGAAGTTGAAATTGGCTATGAAATTAAGAAGTTGTTTGTTGATAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAAC
* * *
73494 TAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTCG
* *
73535 AGTCCAATATCCTTCGCTGTGAAGTTAAAATTGGCTCTG-AATTAGGGAAGTTGCTTT-TTGACA
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATT-GGGAAGTTG-TTTGTTGACA
* ** *
73598 ACCAGCCGTCCCTTCGTTATGAAGTTGAACTTGTGTTGTCTCG
64 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTCG
73641 AGT
1 AGT
73644 GGCACGATAT
Statistics
Matches: 1049, Mismatches: 90, Indels: 36
0.89 0.08 0.03
Matches are distributed among these distances:
94 80 0.08
95 2 0.00
96 2 0.00
99 2 0.00
100 4 0.00
101 3 0.00
104 2 0.00
105 7 0.01
106 944 0.90
107 3 0.00
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (106 bp):
AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAAC
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTCG
Found at i:75258 original size:8 final size:8
Alignment explanation
Indices: 75240--75310 Score: 56
Period size: 8 Copynumber: 8.4 Consensus size: 8
75230 TTTTTGTCCC
75240 TTTTC-TT
1 TTTTCTTT
75247 TTTTCTTT
1 TTTTCTTT
75255 TTTTCTTT
1 TTTTCTTT
75263 CTTTAT-TTT
1 -TTT-TCTTT
75272 GTTTTCTTCTT
1 -TTTTC-T-TT
*
75283 TTTTGCTTC
1 TTTT-CTTT
75292 TTTTCTTT
1 TTTTCTTT
*
75300 TTTTGTTT
1 TTTTCTTT
75308 TTT
1 TTT
75311 GCCATTTTTG
Statistics
Matches: 53, Mismatches: 4, Indels: 13
0.76 0.06 0.19
Matches are distributed among these distances:
7 5 0.09
8 24 0.45
9 14 0.26
10 7 0.13
11 3 0.06
ACGTcount: A:0.01, C:0.13, G:0.04, T:0.82
Consensus pattern (8 bp):
TTTTCTTT
Found at i:75271 original size:28 final size:28
Alignment explanation
Indices: 75240--75294 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
75230 TTTTTGTCCC
*
75240 TTTTCTTTT-TTCTTTTTTTCTTTCTTTA
1 TTTTCTTTTCTTCTTTTTTGC-TTCTTTA
*
75268 TTTTGTTTTCTTCTTTTTTGCTTCTTT
1 TTTTCTTTTCTTCTTTTTTGCTTCTTT
75295 TCTTTTTTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 14 0.58
29 10 0.42
ACGTcount: A:0.02, C:0.15, G:0.04, T:0.80
Consensus pattern (28 bp):
TTTTCTTTTCTTCTTTTTTGCTTCTTTA
Found at i:75300 original size:29 final size:28
Alignment explanation
Indices: 75239--75300 Score: 72
Period size: 29 Copynumber: 2.2 Consensus size: 28
75229 TTTTTTGTCC
*
75239 CTTTTCTTTTTTCTTTTTTTCTTTCTTT
1 CTTTTCTTTTTTCTTTTTTGCTTTCTTT
* *
75267 ATTTTGTTTTCTTCTTTTTTGC-TTCTTTT
1 CTTTTCTTTT-TTCTTTTTTGCTTTC-TTT
75296 CTTTT
1 CTTTT
75301 TTTGTTTTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
28 11 0.39
29 17 0.61
ACGTcount: A:0.02, C:0.16, G:0.03, T:0.79
Consensus pattern (28 bp):
CTTTTCTTTTTTCTTTTTTGCTTTCTTT
Found at i:79703 original size:22 final size:22
Alignment explanation
Indices: 79678--79734 Score: 61
Period size: 19 Copynumber: 2.8 Consensus size: 22
79668 AAATATAATG
79678 AAAATAAATAAATAGTATAAAT
1 AAAATAAATAAATAGTATAAAT
*
79700 AAAAT-AATAAA-A-TATATAT
1 AAAATAAATAAATAGTATAAAT
*
79719 AAAA-ATATAAAT-GTAT
1 AAAATAAATAAATAGTAT
79735 GTATAATATA
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
19 15 0.50
20 4 0.13
21 6 0.20
22 5 0.17
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.30
Consensus pattern (22 bp):
AAAATAAATAAATAGTATAAAT
Found at i:79769 original size:29 final size:27
Alignment explanation
Indices: 79704--79777 Score: 73
Period size: 28 Copynumber: 2.7 Consensus size: 27
79694 ATAAATAAAA
79704 TAATAA-AATATATATAAAAATATAAATG
1 TAATAATAATATA-AT-AAAATATAAATG
*
79732 T-ATGTATAATATAATAAAATACTAAATAG
1 TAAT-AATAATATAATAAAATA-TAAAT-G
79761 TAATAATAATA-AATAAA
1 TAATAATAATATAATAAA
79778 TGAAAAATAA
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
27 8 0.21
28 15 0.38
29 14 0.36
30 2 0.05
ACGTcount: A:0.62, C:0.01, G:0.04, T:0.32
Consensus pattern (27 bp):
TAATAATAATATAATAAAATATAAATG
Found at i:80588 original size:37 final size:37
Alignment explanation
Indices: 80495--80596 Score: 141
Period size: 37 Copynumber: 2.8 Consensus size: 37
80485 ATGCTTGTGG
* * ** * *
80495 ATCCTATCTTTAGGAGTTTAAATAATAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAACTCT
*
80532 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAACTCT
80569 ATCCTATTTTTAGGAGTTTGAATCCTAG
1 ATCCTATTTTTAGGAGTTTGAATCCTAG
80597 TAGGACGAAA
Statistics
Matches: 58, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.40
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAACTCT
Found at i:82345 original size:36 final size:35
Alignment explanation
Indices: 82252--82362 Score: 125
Period size: 35 Copynumber: 3.2 Consensus size: 35
82242 TTGGTTGTTA
* * * * * *
82252 TATAGGAGTGAAATAGTGATAGAAGATGGTAAGGA
1 TATAGGCGTGAAATGGTGATGGAAGATGGTGATGT
* * *
82287 TATAGGCATGCAATGGTAATGGAAGATGGTGATGT
1 TATAGGCGTGAAATGGTGATGGAAGATGGTGATGT
82322 TATAGGCGTGAAAATGGTGATGGAAGATGGTGATGT
1 TATAGGCGTG-AAATGGTGATGGAAGATGGTGATGT
82358 T-TAGG
1 TATAGG
82363 TAGTATCTTA
Statistics
Matches: 63, Mismatches: 12, Indels: 2
0.82 0.16 0.03
Matches are distributed among these distances:
35 39 0.62
36 24 0.38
ACGTcount: A:0.34, C:0.03, G:0.36, T:0.27
Consensus pattern (35 bp):
TATAGGCGTGAAATGGTGATGGAAGATGGTGATGT
Found at i:86346 original size:6 final size:6
Alignment explanation
Indices: 86335--86379 Score: 56
Period size: 7 Copynumber: 7.2 Consensus size: 6
86325 GATGTATGAG
86335 TCTTTT TC-TTT TCTTTT TCTTTTT TCTTCTT TCTTTT TCTCTTT T
1 TCTTTT TCTTTT TCTTTT TC-TTTT TCTT-TT TCTTTT TCT-TTT T
86380 TGTTGCTTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
5 5 0.14
6 14 0.40
7 16 0.46
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (6 bp):
TCTTTT
Found at i:86366 original size:21 final size:22
Alignment explanation
Indices: 86340--86389 Score: 68
Period size: 20 Copynumber: 2.3 Consensus size: 22
86330 ATGAGTCTTT
86340 TTCTTTTCTTTTTCT-TTTTTC
1 TTCTTTTCTTTTTCTCTTTTTC
*
86361 TTC-TTTCTTTTTCTCTTTTTG
1 TTCTTTTCTTTTTCTCTTTTTC
86382 TTGCTTTT
1 TT-CTTTT
86390 GTTGCAGCAC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
20 11 0.44
21 10 0.40
22 1 0.04
23 3 0.12
ACGTcount: A:0.00, C:0.18, G:0.04, T:0.78
Consensus pattern (22 bp):
TTCTTTTCTTTTTCTCTTTTTC
Found at i:86786 original size:35 final size:34
Alignment explanation
Indices: 86747--86846 Score: 92
Period size: 35 Copynumber: 2.8 Consensus size: 34
86737 TGGTGGTTAT
86747 ATAGGCGTGAAATGGTGATAGAATATGGTAAGGAA
1 ATAGGCGTGAAATGGTGAT-GAATATGGTAAGGAA
* * * * * **
86782 ATAGGCGTGCAATGGTAATGTATGATGGTGATGTT
1 ATAGGCGTGAAATGGTGATGAAT-ATGGTAAGGAA
*
86817 ATAGGCGTGAAAATGGTGATGGAAGATGGT
1 ATAGGCGTG-AAATGGTGAT-GAATATGGT
86847 GATGCTTAGG
Statistics
Matches: 51, Mismatches: 11, Indels: 5
0.76 0.16 0.07
Matches are distributed among these distances:
34 3 0.06
35 33 0.65
36 13 0.25
37 2 0.04
ACGTcount: A:0.33, C:0.04, G:0.36, T:0.27
Consensus pattern (34 bp):
ATAGGCGTGAAATGGTGATGAATATGGTAAGGAA
Done.